It is possible, but very unlikely. The best time to do it is now, if it's freshly finished. I have in the past had to go back and do spot repairs on floors that we just finished, usually scratched by the movers.
There are alot of variables though. What type of finish was applied? Dark stain? Is it an inconspicuous area? How did you determine the cause of the poor stain job? Do you see sander marks or is it just inconsistent coloring?
There is alot to be considered, and I would definitely recommend having another professional look at it or push the issue with your current contractor. Sand/finishing is a challenge for most novices, spot repairs are d!@% near impossible.